********************************************************************************
*                               PCONS                                          *
* Calculates structral consensus for all models in a specified directory       *
*                                                                              *
* Reference: Bjorn Wallner and Arne Elofsson, Protein Sci., 2006 15(4):900-913 *
* For comments, please email to: bjorn@sbc.su.se                               *
*                                                                              *
* If the program Seg. faults make sure the stacksize is unlimited:             *
* bash: ulimit -s unlimited                                                    *
* tcsh: limit stacksize unlimited                                              *
*                                                                              *
********************************************************************************


INSTALLATION
============
The package contains a compiled binary in PCONS/bin/

If you like to recompile just do 'make' in the PCONS/ directory

If you have a 64 bit machine you will get some warnings but it still works...

Before you run the program you need to set the stacksize to unlimited.

In bash (with $ as the prompt):
	$ ulimit -s unlimited 
In tcsh
	$ limit stacksize unlimited  

You could add this to your .bashrc or .tschrc.


RUNNING
=======

Usage: pcons    -d <directory w/ models>
                -i <inputfile containing full path to models (one one each line) OBS the filenames w/o path must by unique>
                -casp <output local rmsd as local quality (default is average local S-score)>
                -lgscore <output average LGscore as global quality measure (default is average S-score)>
                -L <target sequence length. default: longest sequence in the set>
                -t <target id, default: will look for T0XXX in the beginning of filenames >


Pcons can take two types of input:
	1) a directory with pdbfiles
	2) a list of pdbfiles

Normally you don't want to compare models from the same method to tell
pcons which method a model is from you should add AUTHOR to the
beginning of your pdbfile.

If the AUTHOR field is missing, pcons will compare that model to all
other models.

The output is a CASP quality assessment format: PFRMAT QA in QMODE 2.

Example
$ bin/pcons -d small_set/